Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31139654", "kind": "science-record", "revision": 8, "content_hash": "sha256:d312541d3d56e84471791f4394eabb955291c4bdfc05034d2847ce1d3ccc4b0a", "created_at": "2026-11-01T15:40:45Z", "updated_at": "2026-11-01T22:43:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes.", "doi": "10.1155/2019/8340573", "pmid": "31139654", "authors": ["Zhaoyan Li", "Lei Zhong", "Zhenwu Du", "Gaoyang Chen", "Jing Shang", "Qiwei Yang", "Qingyu Wang", "Yang Song", "Guizhen Zhang"], "journal": "BioMed research international", "year": 2019, "abstract": "BACKGROUND: Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis.\nMETHODS: The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system.\nRESULTS: A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).", "claims": [{"id": "claim-method", "statement": "The limma package in R was used to identify the DEGs between osteoarthritis synovial membranes and normal synovial membranes [8]. Background adjustment, normalization, and summarization were all included in the process of preprocessing. P values were adjusted using the Hochberg and Benjamini test, and p<0.05 and gene count >2 were set as the cut-off point.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31139654", "locator": "sections[4] \"2.2. Data Preprocessing and DEG Screening\" paragraph 2", "quote": "The limma package in R was used to identify the DEGs between osteoarthritis synovial membranes and normal synovial membranes [8]. Background adjustment, normalization, and summarization were all included in the process of preprocessing. P values were adjusted using the Hochberg and Benjamini test, and p<0.05 and gene count >2 were set as the cut-off point."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data used to support the findings of this study have been deposited in the GEO database (dataset ID:GSE89408), which have been cited.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31139654", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The microarray data used to support the findings of this study have been deposited in the GEO database (dataset ID:GSE89408), which have been cited."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31139654"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE89408"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE89408"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31139654", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2019/8340573", "sha256": "sha256:d98685aa829c4919795720ee7eabf0f5bb09e270a74cdd100db499f61a04cca5", "bytes": 16015, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2019/8340573", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6500622", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE89408", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89408", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE89408", "version": null, "note": "The microarray data used to support the findings of this study have been deposited in the GEO database (dataset 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RESULTS: A total of 229 DEGs were id", "lo Alto, CA, USA), and a QuantStudio™ 7 Flex real-time PCR system (Applied Biosystems, Carlsbad, CA, US"], "order_basis": "paper_text_order:866", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma package in R was used to identify the DEGs between osteoarthritis synovial membranes and normal synovial membranes [8]. Background adjustment, normalization, and summarization were all included in the process of preprocessing. P values were adjusted using the Hochberg and Benjamini test, and p<0.05 and gene count >2 were set as the cut-off point."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}